Functional data analysis approaches for genotype-phenotype association studies from next-generation sequencing

Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^

A case-control study of the association between corneal arcus and death by cardiovascular disease among cornea donors

The cornea of the human eye can develop deposits of lipids in the periphery known as corneal arcus. [2, 10] For over a century, these deposits have been of interest as possible indicators of the accumulation of lipids in arterial walls of the heart and body with implications for heart disease. [2, 10, 11, 29] Heart disease is currently the leading cause of death in this country. [5, 29] There have been several publications suggesting an association between the development of atherosclerotic lesions and corneal arcus. [2, 12, 29] Investigators have differed in their interpretation of the relevance of corneal arcus to coronary heart disease or cardiovascular disease. However, there is widespread consensus that the presence of corneal arcus in patients under the age of 50 should prompt physicians to further investigate for dyslipidemia or heart disease. [2, 3, 6, 8, 19] Earlier studies have often suffered from difficulty in determining the presence or severity of atherosclerosis and from inconsistencies in evaluating corneal arcus. This study involves the review of mortality data, medical and social history and standardized slit lamp examination of corneal tissue donors to evaluate the prevalence of corneal arcus in relation to death by CHD or CVD. The prevalence of arcus, odds ratio, and logistic regression was utilized for statistical analysis.^

Elevated cystatin C & heart failure prognosis a systematic review

Renal insufficiency is one of the most common co-morbidities present in heart failure (HF) patients. It has significant impact on mortality and adverse outcomes. Cystatin C has been shown as a promising marker of renal function. A systematic review of all the published studies evaluating the prognostic role of cystatin C in both acute and chronic HF was undertaken. A comprehensive literature search was conducted involving various terms of 'cystatin C' and 'heart failure' in Pubmed medline and Embase libraries using Scopus database. A total of twelve observational studies were selected in this review for detailed assessment. Six studies were performed in acute HF patients and six were performed in chronic HF patients. Cystatin C was used as a continuous variable, as quartiles/tertiles or as a categorical variable in these studies. Different mortality endpoints were reported in these studies. All twelve studies demonstrated a significant association of cystatin C with mortality. This association was found to be independent of other baseline risk factors that are known to impact HF outcomes. In both acute and chronic HF, cystatin C was not only a strong predictor of outcomes but also a better prognostic marker than creatinine and estimated glomerular filtration rate (eGFR). A combination of cystatin C with other biomarkers such as N terminal pro B- type natriuretic peptide (NT-proBNP) or creatinine also improved the risk stratification. The plausible mechanisms are renal dysfunction, inflammation or a direct effect of cystatin C on ventricular remodeling. Either alone or in combination, cystatin C is a better, accurate and a reliable biomarker for HF prognosis. ^

Association of ALLHAT investigator characteristics with participant recruitment

Clinical trials are often not successful because of the inability to recruit a sufficient number of patients. The Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT), the largest antihypertensive trial ever conducted, provided highly generalized results and successful recruitment of over 42,000 participants. The overall purpose of this study was to examine the association of investigator characteristics with anti-hypertensive (AHT) participant recruitment in ALLHAT. This secondary data analyses collected data from the ALLHAT investigator profile survey and related investigator characteristics to recruitment success. The sample size was 502 investigators, with recruitment data from 37,947AHT participants. Recruitment was dichotomized by categorizing all sites with recruitment numbers at or above the overall median recruitment number of 46 as "Successful Recruitment". Frequency distributions and univariate and multivariate logistic regression were conducted. When adjusting for all other factors, Hispanic ethnicity, suburban setting, Department of Veterans Affairs Medical Centers (VAMC) site type, number of clinical site staff working on the trial, study coordinator hours per week, medical conference sessions attended, the investigator's primary goal and the likelihood that a physician will convince a patient to continue on randomized treatment, have significant impacts on the recruitment success of ALLHAT investigators. Most of the ALLHAT investigators described their primary commitment as being towards their patients and not to scientific knowledge alone. However, investigators that distinguished themselves as leaders in research had greater recruitment success than investigators who were leaders in clinical practice. ALLHAT was a highly successful trial that proved that community based cardiovascular trials can be implemented on a large scale. Exploring characteristics of ALLHAT investigators provides data that can be generalized to sponsors, sites, and others interested in maximizing clinical trial recruitment numbers. Future studies should further evaluate investigator and study coordinator factors that impact cardiovascular clinical trial recruitment success.^

Influencia del ejercicio físico desarrollado durante el embarazo en la respuesta cardiaca fetal = Influence of a physical activity program performed during pregnancy on fetal heart response

INTRODUCCIÓN: El riesgo de padecer enfermedades cardiovasculares y los índices de obesidad infantil han ido en aumento durante los últimos años empobreciendo la salud de la población. La Teoría de Barker relaciona el estado de salud de la madre con el desarrollo fetal, asociando a un deficiente estado físico y hábitos de vida negativos de la mujer embarazada con el aumento del riesgo de padecer cardiopatías en la infancia y adolescencia, así como predisponer al recién nacido a padecer sobrepeso y/u obesidad en su vida posterior. Por otro lado los estudios efectuados sobre ejercicio físico durante el embarazo reportan beneficios para salud materna y fetal. Uno de los parámetros más utilizados para comprobar la salud fetal es su frecuencia cardiaca, mediante la que se comprueba el buen desarrollo del sistema nervioso autónomo. Si se observa este parámetro en presencia de ejercicio materno podría encontrarse una respuesta crónica del corazón fetal al ejercicio materno como consecuencia de una adaptación y mejora en el funcionamiento del sistema nervioso autónomo del feto. De esta forma podría mejorar su salud cardiovascular intrauterina, lo que podría mantenerse en su vida posterior descendiendo el riesgo de padecer enfermedades cardiovasculares en la edad adulta. OBJETIVOS: Conocer la influencia de un programa de ejercicio físico supervisado en la frecuencia cardiaca fetal (FCF) en reposo y después del ejercicio materno en relación con gestantes sedentarias mediante la realización de un protocolo específico. Conocer la influencia de un programa de ejercicio físico en el desarrollo del sistema nervioso autónomo fetal, relacionado con el tiempo de recuperación de la FCF. MATERIAL Y MÉTODO: Se diseñó un ensayo clínico aleatorizado multicéntrico en el que participaron 81 gestantes (GC=38, GE=43). El estudio fue aprobado por el comité ético de los hospitales que participaron en el estudio. Todas las gestantes fueron informadas y firmaron un consentimiento para su participación en el estudio. Las participantes del GE recibieron una intervención basada en un programa de ejercicio físico desarrollado durante la gestación (12-36 semanas de gestación) con una frecuencia de tres veces por semana. Todas las gestantes realizaron un protocolo de medida de la FCF entre las semanas 34-36 de gestación. Dicho protocolo consistía en dos test llevados a cabo caminando a diferentes intensidades (40% y 60% de la frecuencia cardiaca de reserva). De este protocolo se obtuvieron las principales variables de estudio: FCF en reposo, FCF posejercicio al 40 y al 60% de intensidad, tiempo de recuperación de la frecuencia cardiaca fetal en ambos esfuerzos. El material utilizado para la realización del protocolo fue un monitor de frecuencia cardiaca para controlar la frecuencia cardiaca de la gestante y un monitor fetal inalámbrico (telemetría fetal) para registrar el latido fetal durante todo el protocolo. RESULTADOS: No se encontraron diferencias estadísticamente significativas en la FCF en reposo entre grupos (GE=140,88 lat/min vs GC= 141,95 lat/min; p>,05). Se encontraron diferencias estadísticamente significativas en el tiempo de recuperación de la FCF entre los fetos de ambos grupos (GE=135,65 s vs GC=426,11 s esfuerzo al 40%; p<,001); (GE=180,26 s vs GC=565,61 s esfuerzo al 60%; p<,001). Se encontraron diferencias estadísticamente significativas en la FCF posejercicio al 40% (GE=139,93 lat/min vs GC=147,87 lat/min; p<,01). No se encontraron diferencias estadísticamente significativas en la FCF posejercicio al 60% (GE=143,74 lat/min vs GC=148,08 lat/min; p>,05). CONLUSIÓN: El programa de ejercicio físico desarrollado durante la gestación influyó sobre el corazón fetal de los fetos de las gestantes del GE en relación con el tiempo de recuperación de la FCF. Los resultados muestran un posible mejor funcionamiento del sistema nervioso autónomo en fetos de gestantes activas durante el embarazo. ABSTRACT INTRODUCTION: The risk to suffer cardiovascular diseases and childhood obesity index has grown in the last years worsening the health around the population. Barker´s Theory related maternal health with fetal development establishing an association between a poorly physical state and an unhealthy lifestyle in the pregnant woman with the risk to suffer heart disease during childhood and adolescence, childhood overweight and/or obese is related to maternal lifestyle. By the other way researches carried out about physical exercise and pregnancy show benefits in maternal and fetal health. One of the most studied parameters to check fetal health is its heart rate, correct fetal autonomic nervous system development and work is also corroborated by fetal heart rate. Looking at this parameter during maternal exercise a chronic response of fetal heart could be found due to an adaptation and improvement in the working of the autonomic nervous system. Therefore its cardiovascular health could be enhanced during its intrauterine life and maybe it could be maintained in its posterior life descending the risk to suffer cardiovascular diseases in adult life. OBJECTIVES: To know the influence of a supervised physical activity program in the fetal heart rate (FHR) at rest, FHR after maternal exercise related to sedentary pregnant women by a FHR assessment protocol. To know the influence of a physical activity program in the development of the autonomic nervous system related to FHR recovery time. MATERIAL AND METHOD: A multicentric randomized clinical trial was design in which 81 pregnant women participated (CG=38, EG=43). The study was approved by the ethics committee of all of the hospitals participating in the study. All of the participants signed an informed consent for their participation in the study. EG participants received an intervention based on a physical activity program carried out during gestation (12-36 gestation weeks) with a three days a week frequency. All of the participants were tested between 34-36 weeks of gestation by a specific FHR assessment protocol. The mentioned protocol consisted in two test performed walking and at a two different intensities (40% and 60% of the reserve heart rate). From this protocol we obtained the main research variables: FHR at rest, FHR post-exercise at 40% and 60% intensity, and FHR recovery time at both walking test. The material used to perform the protocol were a FH monitor to check maternal HR and a wireless fetal monitor (Telemetry) to register fetal beats during the whole protocol. RESULTS: There were no statistical differences in FHR at rest between groups (EG=140,88 beats/min vs CG= 141,95 beats/min; p>,05). There were statistical differences in FHR recovery time in both walking tests between groups (EG=135,65 s vs CG=426,11 s test at 40% intensity; p<,001); (EG=180,26 s vs CG=565,61 s test at 60% intensity; p<,001). Statistical differences were found in FHR post-exercise at 40% intensity between groups (EG=139,93 beats/min vs CG=147,87 beats/min; p<,01). No statistical differences were found in FHR at rest post-exercise at 60% intensity between groups (EG=143,74 beats/min vs CG=148,08 beats/min; p>,05). CONCLUSIONS: The physical activity program performed during gestation had an influence in fetal heart of the fetus from mother in the EG related to FHR recovery time. These results show a possible enhancement on autonomic nervous system working in fetus from active mothers during gestation.

Endothelin-induced conversion of embryonic heart muscle cells into impulse-conducting Purkinje fibers

A regular heart beat is dependent on a specialized network of pacemaking and conductive cells. There has been a longstanding controversy regarding the developmental origin of these cardiac tissues which also manifest neural-like properties. Recently, we have shown conclusively that during chicken embryogenesis, impulse-conducting Purkinje cells are recruited from myocytes in spatial association with developing coronary arteries. Here, we report that cultured embryonic myocytes convert to a Purkinje cell phenotype after exposure to the vascular cytokine, endothelin. This inductive response declined gradually during development. These results yield further evidence for a role of arteriogenesis in the induction of impulse-conducting Purkinje cells within the heart muscle lineage and also may provide a basis for tissue engineering of cardiac pacemaking and conductive cells.

The association between older age and receipt of care and outcomes in patients with acute coronary syndromes : a cohort study of the Myocardial Ischaemia National Audit Project (MINAP)

Peer reviewed

“You Can't Always Get What You Want” : A Novel Research Paradigm to Explore the Relationship between Multiple Intentions and Behaviours

Funded by •Centre for Translational Research in Public Health •United Kingdom Clinical Research Collaboration Public Health Research Centre •British Heart Foundation •Cancer Research United Kingdom •Economic and Social Research Council •Medical Research Council •National Institute for Health

Angiotensin II type1a receptor gene expression in the heart: AP-1 and GATA-4 participate in the response to pressure overload

Hypertrophy of mammalian cardiac muscle is mediated, in part, by angiotensin II through an angiotensin II type1a receptor (AT1aR)-dependent mechanism. To understand how the level of AT1aRs is altered in this pathological state, we studied the expression of an injected AT1aR promoter-luciferase reporter gene in adult rat hearts subjected to an acute pressure overload by aortic coarctation. This model was validated by demonstrating that coarctation increased expression of the α-skeletal actin promoter 1.7-fold whereas the α-myosin heavy chain promoter was unaffected. Pressure overload increased expression from the AT1aR promoter by 1.6-fold compared with controls. Mutations introduced into consensus binding sites for AP-1 or GATA transcription factors abolished the pressure overload response but had no effect on AT1aR promoter activity in control animals. In extracts from coarcted hearts, but not from control hearts, a Fos-JunB-JunD complex and GATA-4 were detected in association with the AP-1 and GATA sites, respectively. These results establish that the AT1aR promoter is active in cardiac muscle and its expression is induced by pressure overload, and suggest that this response is mediated, in part, by a functional interaction between AP-1 and GATA-4 transcription factors.